PBSalign: Sequence-independent local alignment of protein binding sites

Accurate alignment of protein-protein binding sites can aid in protein docking studies and constructing templates for predicting structure of protein complexes, along with in-depth understanding of evolutionary and functional relationships. However, over the past three decades, structural alignment algorithms have focused predominantly on global alignments with little effort on the alignment of local interfaces. In this paper, we introduce the PBSalign (Protein-protein Binding Site alignment) method, which integrates techniques in graph theory, 3D localized shape analysis, geometric scoring, and utilization of physiochemical and geometrical properties. Computational results demonstrate that PBSalign is capable of identifying similar homologous and analogous binding sites accurately and performing alignments with better geometric match measures than existing protein-protein interface comparison tools. The proportion of better alignment quality generated by PBSalign is 46%, 56%, and 70% more than Align as judged by the average match index (MI), similarity index (SI), and structural alignment score (SAS), respectively. PBSalign provides the life science community a fast and accurate solution to binding-site alignment while striking the balance between topological details and computational complexity.